Martin Scorsese’s “Silence” is a story of faith and anguish. It tells of a Portuguese Jesuit priest, Father Rodrigues, who in 1643 heads into the dark heart of Japan, where Christians are being persecuted — boiled alive, immolated and crucified. Rodrigues (Andrew Garfield) sets out to help keep the church alive in Japan, a mission that perhaps inevitably leads to God. The film’s solemnity is seductive — as is Mr. Scorsese’s art — especially in light of the triviality and primitiveness of many movies, even if its moments of greatness also make its failures seem more pronounced.

Mr. Scorsese’s work has long involved struggles of faith of one kind or another, from the religious guilt that afflicts Harvey Keitel’s thug in “Mean Streets” (“You don’t make up for your sins in the church.”) through that circle of hell known as “The Wolf of Wall Street.” In “Silence” the struggle begins in a mist-wreathed landscape where severed human heads rest on a crude shelf, like trophies of some ghastly victory. Today, decapitations in the name of religion are a gruesome hallmark of Islamist extremists, but here they introduce a dispute involving the Japanese authorities, who, intent on maintaining the country’s power and isolation, are set on eradicating Christianity, its proselytizers and converts.

Figures soon emerge from the mist, notably Father Ferreira (Liam Neeson), who, as gaunt and tormented as any martyred Caravaggio saint, watches in gaping horror as guards ladle water from hot springs on shrieking Christians. Rodrigues learns about this hellish scene from Father Valignano (Ciaran Hinds), who also relates that Ferreira has renounced his religion and is living as “a Japanese.” Rodrigues, having studied with Ferreira, refuses to accept that the older priest’s belief has been shattered and departs for Japan accompanied by another priest, Father Garupe (a fine, underused Adam Driver), and a Japanese guide, Kichijiro (Yosuke Kubozuka, excellent).

The movie’s early scenes are filled with severe pictorial beauty as the pale thermal steam snaking around the martyred Christians gives way to the vaulted white room where the black-clothed Jesuits meet. The chromatic contrast between the inkiness of their cassocks and the room’s ascetic whiteness finds an echo in Rodrigues’s rigid dualism, a belief in absolutes that will be tested. His resoluteness even seems answered by the calm camerawork (no jitters here), which early on is dramatically punctuated by a ravishing overhead shot of the three Jesuit priests gliding down a flight of stony, bleach-white stairs, as if they were being looked down on from high above.

Whether this represents God’s vision or that of the priests, it is very much the point of view of the movie’s own creator. This overhead shot and others suggest that there’s a divine aspect to the priests’ mission, an idea that Mr. Scorsese visually and narratively underlines in the Lazarus-like cave in which Rodrigues and Garupe first take shelter in Japan; in Rodrigues’s self-aggrandizing identification with Jesus; and, crucially, through the figure of Judas. As in Mr. Scorsese’s 1988 film, “The Last Temptation of Christ,” his messy, excitingly alive adaptation of that Nikos Kazantzakis novel, Judas must play a part in “Silence” because without him there can be no Jesus.

Once in Japan, Rodrigues and Garupe make contact with a village of hidden Christians, who live in fear of the authorities and a cobralike smiler known as the Inquisitor, Inoue (Issey Ogata, in one of the film’s strongest performances). By day, the priests hide in a small, cramped hut near the village; by night, they lead their new flock in dimly lighted rooms, delivering sermons in Latin, baptizing children and taking confession. Mr. Scorsese draws some modest, uneasy comedy from the linguistic and cultural differences between the priests and their congregation, as when a grabby, highly agitated woman begs the rather startled Garupe to hear her confession.

Despite the mugging from both confessor and confessed, the exchange feels forced and comes across as a bid to lighten the gloom; if anything, it turns a feverish plea for absolution into a bit of vaudeville. There’s something uncomfortably and literally childlike about this child of God, who, like the other villagers, with their pleading eyes and hands, seems like a relic from a white-savior myth. Kichijiro, who enters grunting and twitching, as if in homage to Toshiro Mifune, and grovels at the priest’s feet, also seems on hand as much for comic relief as for guidance. Yet, even as the film seems to share the outsider perspectives of Rodrigues and Garupe, instructively, it is the village elders — brilliantly played by Yoshi Oida and Shinya Tsukamoto — who give these scenes flesh, bone and pain.

“Silence” is based on the 1966 novel by the Japanese author Shusaku Endo that has attracted heavyweight admirers since it was first published. Graham Greene praised the novel, as did John Updike; for years, Mr. Scorsese tried to turn it into a film. (He wrote the foreword for a recent edition.) Filled with reams of religious dialogue, the novel fictionalizes history — the 17th-century purging of Christianity in Japan — as a means to explore religious faith and cultural difference. What preoccupies Endo is whether Western Christianity can take root in what the Inquisitor describes as “this swamp of Japan,” which seems inhospitable to outside forces. It’s a story of God, nation and myth.

It’s easy to understand Mr. Scorsese’s interest in the novel and specifically in the character of Rodrigues. Despite the priest’s piety, black vestments and narrative prominence, he is no more a Hollywood hero than most of Mr. Scorsese’s falling and fallen men, with their arrogance and vanity. Rodrigues cowers in fear, recoils from his flock and assures himself of the goodness that the church — and he, by extension — has brought. (He pities the worshipers but is proud of his ministering.) His faith, including in himself, sustains Rodrigues, but even as he tends to the souls of the hidden Christians he fails to ease their earthly suffering. God is silent; in a way, so is this most ardent missionary.

The silence of the title resounds insistently; it’s in the screams of the faithful and in Rodrigues’s endless searching. Why, he agonizes with no self-awareness, does God not answer prayers and alleviate suffering, a question which proves too heavy a load for Mr. Garfield’s talents. When he plays against the other actors, he can seem as decorative as a plaster saint (his luxuriously styled hair is right out of a 1950s biblical epic), which makes the other performers and their characters look stronger, and works for the story. Rodrigues is weak. But it’s weakness without depth or the burning belief that would make his errors shattering. When he carries on alone, speaking to God, questioning and suffering at great, monotonous length, his weakness becomes tedious, as does the film.

“Silence” argues against orthodoxy, but its messenger is too pallid. This is less the fault of Mr. Garfield than of Mr. Scorsese’s conception of Rodrigues as the story’s fulcrum instead of its void. Mr. Scorsese fills the film with haunting tableaus and performances — including from Tadanobu Asano, as the Interpreter — that tug from the edges, pulling attention away from its center. In the end, nothing that Rodrigues says resonates as deeply as Inoue’s terrifying, teasing whine, which conveys the larger cultural and political stakes; nothing imparts the mystery of creation as potently as the flicker of a darting emerald lizard or an eerie parade of cats prowling through a spookily deserted village.

These moments shake “Silence” and you too; the movie could use more jolts, more trembling, more surrealism; maybe, as in “The Last Temptation of Christ,” a talking lion to go along with its trippy lizard. “Silence” is as visually striking as you might expect, but also overly tidy, clean and decorous, despite its tortured flesh, its mud and its blood. There’s a crushing lack of urgency to this story and its telling, perhaps because it took Mr. Scorsese, who wrote the script with Jay Cocks, so long to make “Silence.” It’s disappointing because few directors can engage doubt and belief as powerfully as Mr. Scorsese can, but also because doubt and belief have again set the world on fire.